In one version of an orbital electrostatic trap mass analyzer (commercially marketed by Thermo Fisher Scientific under the trademark Orbitrap™) ions are trapped in an orbital motion within a space between an inner, spindle-like electrode and an outer, barrel-like electrode assembly. Different ions oscillate at different frequencies within the orbital electrostatic trap, resulting in their separation over a period of time. The image current from the trapped ions, induced on the outer electrode assembly, is detected and the resulting time-dependent amplitude signal is converted to a frequency spectrum and then to a mass spectrum by processing the data in a manner similar to that used in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The resolving power of an orbital electrostatic trap mass analyzer can be improved by increasing the frequency of ion motion (by, for example, increasing the strength of the electrostatic field) or by increasing the detection period, making it possible to achieve a resolving power up to at least 1,000,000 at m/z 200 using currently commercially available orbital electrostatic trap mass analyzers.
Mass analyzer systems, including orbital electrostatic trap and FTICR systems, require proper tuning in order to optimize the voltages that are applied to the various electrodes of the mass analyzer and associated ion optics. The tuning process may be performed one time only, such as for instance at the time the instrument is initially set-up. After the voltages have been optimized, according to a set of criteria, the voltages may be fixed at the optimized values. Typically, the criteria for which the voltages are optimized correspond to high-stress scenarios, e.g., highest permitted resolving power, largest permitted ion population, etc. The rationale for tuning based on high-stress scenarios criteria stems from the fact that the analytical metrics of orbital electrostatic trap and FTICR mass spectra (e.g., resolving power, signal-to-noise ratio, etc.) are determined by the trajectories of the ions that are captured in the analyzer, and how well those trapped ions adhere to certain simplified equations of motion. In particular, the longer the ions are allowed to undergo orbital motion, the better the resolving power. However, it is also generally the case that any deviations in ion motion from the idealized trajectories will be magnified proportional to the amount of time the ions spend in the analyzer. It therefore follows that if ion motion is close-to-ideal for long transients (high resolving power), then it will also be close-to-ideal for shorter transients (lower resolving power).
This traditional approach to tuning an orbital electrostatic trap or FTICR mass analyzer, using optimization criteria that are selected for high-stress scenarios, generally ignores two important realities. First, a majority of users do not operate the instrument at the highest possible resolving power settings. This is especially true in typical proteomics experiments, where the resolving power setting might be only 120,000 (at m/z 200), a factor of at least 2 less than the setting at which the instrument was tuned. Higher resolving powers are not used because the added data does not typically result in analytically useful gains for experiments in which the most important result is the number of peptide identifications. Second, any defects in the analyzer may only be apparent at the longest transient times (highest resolving power settings). Accordingly, the traditional tuning approach optimizes mass analyzer properties that are rarely or never encountered in practice when the instrument is operated using lower resolving power settings.
It would be beneficial to provide methods and apparatus that overcome at least some of the above-mentioned disadvantages and/or limitations.